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In silico design and in vivo implementation of yeast gene Boolean gates.

Marchisio MA - J Biol Eng (2014)

Bottom Line: Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required.Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits.As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

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Affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland. marchisio@hit.edu.cn.

ABSTRACT
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

No MeSH data available.


OR gates based on distributed output architecture. A) tet OR NOT(estr)–IMPLY logic function. B) tet OR IPTG. For both circuits, measured and expected fluorescence output levels are reported. Notice that YES tetOp gates inside both OR gates differ from the one in Table1 since their plasmid vectors do not carry the HIS3 marker (see Additional file1: Table S3, for more details).
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Figure 7: OR gates based on distributed output architecture. A) tet OR NOT(estr)–IMPLY logic function. B) tet OR IPTG. For both circuits, measured and expected fluorescence output levels are reported. Notice that YES tetOp gates inside both OR gates differ from the one in Table1 since their plasmid vectors do not carry the HIS3 marker (see Additional file1: Table S3, for more details).

Mentions: We implemented two OR gates: "tet OR NOT(estr)" and "tet OR IPTG". Both circuits show a good agreement between measured and computed fluorescence outputs (see Figure7). Moreover, their 0/1 thresholds (4000 and 4250 AU, respectively) could be determined prior to the experiments, on the sole basis of their YES/NOT components’ digital behavior. Although, as expected, the 1 output levels are uneven and the 0 one is rather high, the significant signal separation registered from both circuits (3983 and 3738 AU, respectively) guarantees a clear reproduction of the OR gates’ truth table.


In silico design and in vivo implementation of yeast gene Boolean gates.

Marchisio MA - J Biol Eng (2014)

OR gates based on distributed output architecture. A) tet OR NOT(estr)–IMPLY logic function. B) tet OR IPTG. For both circuits, measured and expected fluorescence output levels are reported. Notice that YES tetOp gates inside both OR gates differ from the one in Table1 since their plasmid vectors do not carry the HIS3 marker (see Additional file1: Table S3, for more details).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3926364&req=5

Figure 7: OR gates based on distributed output architecture. A) tet OR NOT(estr)–IMPLY logic function. B) tet OR IPTG. For both circuits, measured and expected fluorescence output levels are reported. Notice that YES tetOp gates inside both OR gates differ from the one in Table1 since their plasmid vectors do not carry the HIS3 marker (see Additional file1: Table S3, for more details).
Mentions: We implemented two OR gates: "tet OR NOT(estr)" and "tet OR IPTG". Both circuits show a good agreement between measured and computed fluorescence outputs (see Figure7). Moreover, their 0/1 thresholds (4000 and 4250 AU, respectively) could be determined prior to the experiments, on the sole basis of their YES/NOT components’ digital behavior. Although, as expected, the 1 output levels are uneven and the 0 one is rather high, the significant signal separation registered from both circuits (3983 and 3738 AU, respectively) guarantees a clear reproduction of the OR gates’ truth table.

Bottom Line: Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required.Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits.As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland. marchisio@hit.edu.cn.

ABSTRACT
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.

No MeSH data available.